Oligonucleotide analogs are useful as tools in molecular biology, as diagnostics, and as potential therapeutic agents. Peptide nucleic acids (PNAs) are DNA analogs that have received a lot of attention in regard to their high affinity for complementary sequences on RNA and DNA both in a single and double stranded forms (Nielsen, et al. (1991) Science 254:1497-1500; Hyrup and Nielsen (1996) Bioorg. Med. Chem. 4:5-23; Uhlmann, et al. (1998) Angew. Chem. Int. Ed. 37:2796-2823). Their therapeutic potential for gene-specific, nontoxic, and non-immunogenic therapy has been limited as nucleic acid binding agents due to poor uptake into mammalian cells (Koppelhus and Nielsen (2003) Adv. Drug Deliv. Rev. 55:267-280). The synthesis of modified PNA or PNA conjugates presents new means of improving the cellular uptake and developing artificial chemical nucleases. For example, PNAs conjugated to diethylenetriamine and neocuproine Zn(II) derivatives are able to hydrolyze RNA targets in vitro (Verheijen, et al. (2000) Angew. Chem. Int. Ed. 39:369-372; Whitney, et al. (2003) S. Chem. Commun. 1:36-37).
In vivo studies using microinjection (Hanvey, et al. (1992) Science 258:1481-1485) and carrier peptides (Cutrona, et al. (2000) Nature Biotech. 18:300-303) or guanidine-based PNA (Zhou, et al. (2003) J. Am. Chem. Soc. 125:6878-6879) have been described. A membrane-permeating peptide conjugated to a PNA targeting the transactivation response element (TAR) of HIV-1 has been shown to inhibit HIV-1 production when supplemented in HIV-1 infected cell culture (Kaushik, et al. (2002) J. Virol. 76:3881-3891).
Aminoglycoside antibiotics such as neomycin B bind specifically to 16S bacterial ribosomal RNA (rRNA) and perturb protein synthesis (Koppelhus and Nielsen (2003) supra). Neomycin also binds to the HIV RNA recognition elements, RRE (Rev Responsive Element).(Zapp, et al. (1993) Cell 74:969-978) and TAR (Mei, et al. (1995) Bioorg. Med. Chem. Lett. 5:2755-2760) and blocks in vitro the HIV-Rev and HIV-Tat RNA-protein interactions necessary for transactivation. Unfortunately, neomycin B is toxic and high level antibiotic resistance that involves enzymatic modifications have been reported (Mingeot-Leclerc, et al. (1999) Antimicrob. Agents Chemother. 43:727-737; Mingeot-Leclerc and Tulkens (1999) Antimicrob. Agents Chemother. 43:1003-1012; Kotra, et al. (2000) Antimicrob. Agents Chemother. 44:3249-3256). Detailed comparative biochemical experiments, NMR studies and/or molecular modelling have shown that rings I and II of neomycin-class aminoglycosides, corresponding to the neamine structure, are essential structural elements involved in the specific binding to rRNA (Fourmy, et al. (1998) J. Mol. Biol. 277:347-362), RRE (Leclerc and Cedergren (1998) J. Med. Chem. 41:175-182) and TAR RNA (Hermann and Westhof (1999) J. Med. Chem. 42:1250-1261). New chemistries have been developed to synthesize small antiviral or antibiotic agents from neamine (Greenberg, et al. (1999) J. Am. Chem. Soc. 121:6527-6541; Park, et al. (1996) J. Am. Chem. Soc. 118:10150-10155). The high affinity of polycationic aminoglycosides to DNA was recently used successfully in oligo-2′-deoxyribonucleotides (ODN) transfection into cells for developing gene therapy (Belmont, et al. (2002) J. Gene Med. 4:517-526) and the synthesis of ODN-aminoglycoside conjugates were reported (Charles, et al. (2003) Bioorg. Med. Chem. Lett. 13:1607). In vitro, aminoglycosides are able to stabilize nucleic acid triple helices (Arya, et al. (2003) J. Am. Chem. Soc. 125:3733-3744) and aminoglycoside-copper (II) complexes are very efficient artificial nucleases which hydrolyze RNA (Sreedhara, et al. (1999) A. Chem. Commun. 1147-1148) or DNA (Sreedhara, et al. (2000) J. Am. Chem. Soc. 122:8814-8824).
WO 00/39139 teaches aminoglyoside-arginine conjugates wherein the aminoglycoside antibiotic is preferably kanamycin, gentamycin or neomycin that is conjugated to arginine residues.
Neamine derivatives have been prepared in modifying the amino functions, or the 3′-, the 5- or the 6- hydroxyl function in order to increase the affinity for the RNA targets and/or to induce a resistance to aminoglycoside-modifying enzymes (Kotra, et al. (2000) Antimicrob. Agents Chemother. 3249-3256; Kotra and Mobashery (2001) Curr. Org. Chem. 5:193-205). Combinatorial chemistry has been used to generate neamine libraries of neomycin B “mimetics” by selective modifications at the 5 position (Park, et al. (1996) J. Am. Chem. Soc. 118:10150-10155; Greenberg, et al. (1999) J. Am. Chem. Soc. 121:6527-6541; Sucheck, et al. (2000) Angew. Chem. Int. Ed. 39:1080-1084; Sucheck, et al. (2000) J. Am. Chem. Soc. 122:5230-5231). Dimers of neamine have been obtained in which the two subunits are linked by an amino chain attached at the 5-positions such they target rRNA and inhibit resistance causing enzymes (Sucheck, et al. (2000) supra). Aminoglycosides and neamine have also been modified in order to decrease the strength of their electrostatic interactions with aminoglycoside 3′-phosphotransferases types Ia and IIa, responsible for the resistance (Roestamadjli, et al. (1995) J. Am. Chem. Soc. 117:80-84; Roestamadjli, et al. (1995) J. Am. Chem. Soc. 117:11060-11069; Roestamadjli and Mobashery (1998) Bioorg. Med. Chem. Lett. 8:3483-3488; Liu, et al. (2000) J. Org. 
Chem. 65:7422-7431). Neamine derivatives possessing an amino side chain at the 6-position have been synthesised and some of these compounds are very poor substrates for two important purified resistance enzymes while exhibiting interesting antibiotic properties (Haddad, et al. (2002) J. Am. Chem. Soc. 124:3229-3237).